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I like gen 1 more than any nugen game (starting with Ruby/Sapphire), but consider the following:
>an evil team led by Sakaki/Giovanni aims for world domination
>for this purpose, they first steal fucking SILPH SCOPE and you're required to retrieve it to progress
>then Giovanni says "you can keep the SILPH SCOPE (how it was supposed to help our plans anyway?)" and infiltrates SILPH CO., a company that produces Poke Balls and SILPH SCOPEs, among other things
>controlling this company somehow makes you the ruler of the world (does this mean that the current SILPH president is one?)
>Giovanni loses a Pokemon battle
>the curtain comes down
You have to agree this sounds pretty convoluted, and all fan attempts to explain the plot always end up with Giovanni aiming to get his hands on Master Ball and catch Mewtwo while being also involved in its creation. In other words, a plot where evil team leader tries to use a powerful Pokemon to reach some goal.
You can believe or dismiss these theories, either way there's nothing inherently wrong with a legendary/strong Pokemon being a part of the plot. If anything, it makes sense considering the context and implications of a Pokemon world, where godlike creatures exist and tempt evil people to utilize their powers.
I think execution is what matters way more, and this is where newer games fall short, holding players' hands as they walk through colorful and safe 0theme parks to face yet another goofy villain.
